ADVANCED MAGNETICS INC
SC 13D/A, 1997-12-24
IN VITRO & IN VIVO DIAGNOSTIC SUBSTANCES
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<PAGE>
 
                      SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, DC  20549

                                --------------

                                 SCHEDULE 13D
                                (RULE 13d-101)

                   UNDER THE SECURITIES EXCHANGE ACT OF 1934
                             (AMENDMENT NO. 2)/1/


                           ADVANCED MAGNETICS, INC.
                           ------------------------
                               (Name of Issuer)

                                 Common Stock
                                 ------------
                        (Title of Class of Securities)

                                  00753 P 103
                                  -----------
                                (CUSIP Number)

                                  Hope Flack
                               BVF Partners L.P.
                       333 West Wacker Drive, Suite 1600
                           Chicago, Illinois  60606
                                (312) 263-7777
                 --------------------------------------------
                 (Name, Address and Telephone Number of Person
               Authorized to Receive Notices and Communications)

                               November 28, 1997
                               -----------------
            (Date of Event which Requires Filing of this Statement)

     If the filing person has previously filed a statement on Schedule 13G to
report the acquisition which is the subject of this Schedule 13D, and is filing
this schedule because of Rule 13d-1(b)(3) or (4), check the following box [ ].

        Note: Six copies of this statement, including all exhibits, should be
filed with the Commission. See Rule 13d-1(a) for other parties to whom copies
are to be sent.

                        (Continued on following pages)

                             (Page 1 of 7 Pages)

- -------------------------
/1/    The remainder of this cover page shall be filled out for a reporting
person's initial filing on this form with respect to the subject class of
securities, and for any subsequent amendment containing information which would
alter disclosures provided in a prior cover page.
                                        
       The information required on the remainder of this cover page shall not be
deemed to be "filed" for the purpose of Section 18 of the Securities Exchange
Act of 1934 or otherwise subject to the liabilities of that section of the Act
but shall be subject to all other provisions of the Act (however, see the
Notes).
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 00753 P 103         SCHEDULE 13D               PAGE 2 OF 7 PAGES
- -----------------------                                  ---------------------
 
- ------------------------------------------------------------------------------
      NAME OF REPORTING PERSON
 1    S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
      
      BIOTECHNOLOGY VALUE FUND, L.P.

- ------------------------------------------------------------------------------
      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
 2                                                              (a) [_]
                                                                (b) [_]
- ------------------------------------------------------------------------------
      SEC USE ONLY
 3
 
- ------------------------------------------------------------------------------
      SOURCE OF FUNDS*
 4    
           WC
- ------------------------------------------------------------------------------
      CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO
 5    ITEMS 2(d) or 2(e)                                                   [_]
 
- ------------------------------------------------------------------------------
      CITIZENSHIP OR PLACE OF ORGANIZATION
 6    
      DELAWARE

- ------------------------------------------------------------------------------
                          SOLE VOTING POWER
                     7   
     NUMBER OF                -0-   
 
      SHARES       -----------------------------------------------------------
                          SHARED VOTING POWER
   BENEFICIALLY      8
                             335,500
     OWNED BY
                   -----------------------------------------------------------
       EACH               SOLE DISPOSITIVE POWER
                     9    
    REPORTING                -0-    
 
      PERSON       -----------------------------------------------------------
                          SHARED DISPOSITIVE POWER
       WITH         10
                             335,500
- ------------------------------------------------------------------------------
      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
11  
         335,500

- ------------------------------------------------------------------------------
      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*
12                  
          [_]            
- ------------------------------------------------------------------------------
      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
13    
       4.9%

- ------------------------------------------------------------------------------
      TYPE OF REPORTING PERSON*
14
      PN

- ------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 00753 P 103          SCHEDULE 13D               PAGE 3 OF 7 PAGES
- -----------------------                                  ---------------------
 
- ------------------------------------------------------------------------------
      NAME OF REPORTING PERSON
 1    S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
      
      BVF PARTNERS L.P. 

- ------------------------------------------------------------------------------
      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
 2                                                              (a) [_]
                                                                (b) [_]
- ------------------------------------------------------------------------------
      SEC USE ONLY
 3
 

- ------------------------------------------------------------------------------
      SOURCE OF FUNDS*
 4    
      00
- ------------------------------------------------------------------------------
      CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO
 5    ITEMS 2(d) or 2(e)                                                   [_]
 
- ------------------------------------------------------------------------------
      CITIZENSHIP OR PLACE OF ORGANIZATION
 6    
      DELAWARE
- ------------------------------------------------------------------------------
                          SOLE VOTING POWER
                     7   
     NUMBER OF                -0-   
 
      SHARES       -----------------------------------------------------------
                          SHARED VOTING POWER
   BENEFICIALLY      8
                          
     OWNED BY                 665,335
                   -----------------------------------------------------------
       EACH               SOLE DISPOSITIVE POWER
                     9    
    REPORTING                 -0-   
 
      PERSON       -----------------------------------------------------------
                          SHARED DISPOSITIVE POWER
       WITH         10
                             665,335
- ------------------------------------------------------------------------------
      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
11  
         665,335

- ------------------------------------------------------------------------------
      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*
12                  
                [_]
- ------------------------------------------------------------------------------
      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
13    
       9.8%

- ------------------------------------------------------------------------------
      TYPE OF REPORTING PERSON*
14
      PN

- ------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 00753 P 103         SCHEDULE 13D               PAGE 4 OF 7 PAGES
- -----------------------                                  ---------------------
 
- ------------------------------------------------------------------------------
      NAME OF REPORTING PERSON
 1    S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
      
         BVF INC.       

- ------------------------------------------------------------------------------
      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
 2                                                              (a) [_]
                                                                (b) [_]
- ------------------------------------------------------------------------------
      SEC USE ONLY
 3
 

- ------------------------------------------------------------------------------
      SOURCE OF FUNDS*
 4    
         WC, 00
- ------------------------------------------------------------------------------
      CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO
 5    ITEMS 2(d) or 2(e)                                                   [_]
 
- ------------------------------------------------------------------------------
      CITIZENSHIP OR PLACE OF ORGANIZATION
 6    
          DELAWARE

- ------------------------------------------------------------------------------
                          SOLE VOTING POWER
                     7   
     NUMBER OF                -0-   
 
      SHARES       -----------------------------------------------------------
                          SHARED VOTING POWER
   BENEFICIALLY      8
                          
     OWNED BY                 665,335
                   -----------------------------------------------------------
       EACH               SOLE DISPOSITIVE POWER
                     9    
    REPORTING                  -0-   
 
      PERSON       -----------------------------------------------------------
                          SHARED DISPOSITIVE POWER
       WITH         10
                              665,335
- ------------------------------------------------------------------------------
      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
11  
         665,355

- ------------------------------------------------------------------------------
      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*
12                  
                [_]
- ------------------------------------------------------------------------------
      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
13    
       9.8%

- ------------------------------------------------------------------------------
      TYPE OF REPORTING PERSON*
14
      IA, CO

- ------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 00753 P 103         SCHEDULE 13D               PAGE 5 OF 7 PAGES
- -----------------------                                  ---------------------

        This Amendment No. 2 (this "Amendment") relates to the Statement on
Schedule 13D, dated October 30, 1996, as amended by Amendment No. 1, dated April
18, 1997 (as so amended, the "Statement"), filed with the Securities and
Exchange Commission on behalf of Biotechnology Value Fund, L.P., a Delaware
limited partnership ("BVF"), BVF Partners L.P., a Delaware limited partnership
("Partners"), and BVF Inc., a Delaware corporation ("BVF Inc." and, together
with BVF and Partners, the "Reporting Persons") with respect to the Common
Stock, par value $0.01 per share (the "Stock"), of Advanced Magnetics, Inc.
("Advanced Magnetics"). The principal executive office of Advanced Magnetics is
located at 725 Concord Ave, Cambridge, MA 02138.

        Item 3 is hereby amended to read in its entirety as follows:

ITEM 3.   SOURCE AND AMOUNT OF FUNDS OR OTHER CONSIDERATION.

        Since November 3, 1997, Partners, in its capacity as general partner of
BVF, has purchased on behalf of such limited partnership an aggregate number of
57,480 shares of the Stock for an aggregate consideration of $536,540.95,
utilizing funds provided by BVF from its working capital pursuant to the terms
of its limited partnership agreement with Partners. In addition, Partners, in
its capacity as investment manager with respect to certain managed accounts, has
purchased on behalf of such managed accounts an aggregate number of 76,255
shares of the Stock for an aggregate consideration of $698,863.01, utilizing
funds under management by Partners pursuant to an investment management
agreement between Partners and such managed accounts.

 
        Item 5 is hereby amended to read in its entirety as follows:

ITEM 5.   INTEREST IN SECURITIES OF THE ISSUER.

     (a) BVF beneficially owns 335,500 shares of the Stock, Partners
beneficially owns 665,335 shares of the Stock, and BVF Inc. beneficially owns
665,335 shares of the Stock, approximately 4.9%, 9.8% and 9.8%, respectively, of
the aggregate number of shares outstanding (as reported in Advanced Magnetics
most recent quarterly statement on Form 10-Q).

     (b) BVF shares voting and dispositive power over the 335,500 shares of the
Stock it beneficially owns with Partners.  Partners and BVF Inc. share voting
and dispositive power over the 665,335 shares of the Stock they beneficially own
with, in addition to BVF, the managed accounts on whose behalf Partners, as
investment manager, purchased such shares. The managed accounts on whose behalf
Partners owns shares of the Stock are Investment 10 L.L.C., an Illinois limited
liability company ("ILL10"), Palamundo, L.D.C., a limited duration company
organized under the laws of the Cayman Islands ("Palamundo"), ZPG 
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 00753 P 103         SCHEDULE 13D               PAGE 6 OF 7 PAGES
- -----------------------                                  ---------------------

Securities, L.L.C., a New York limited liability company ("ZPG") and
Biotechnology Value Fund, Ltd., a Cayman Islands Corporation ("BVF Ltd.").
ILL10, Palamundo, ZPG and BVF Ltd. are collectively referred to herein as the
"Accounts." The Accounts specialize in holding biotechnology stocks for
investment purposes and the business address of each is BVF Partners L.P., 333
West Wacker Drive, Suite 1600, Chicago, Illinois 60606.

     (c) Exhibit B attached hereto contains information as to all transactions
in the Stock by the Reporting Persons during the past 60 days.  All such
transactions were made for cash in open market, over-the-counter transactions.
No other transactions in the Stock have been effected by the Reporting Persons
during the past 60 days.

     (d) The Accounts are entitled to receive dividends and any sale proceeds
with respect to the Stock in proportion to their respective ownership interests
therein.

     Item 7 is hereby amended to read in its entirety as follows:

ITEM 7.   MATERIAL TO BE FILED AS EXHIBITS.

     Exhibit A - Agreement Regarding Joint Filing

     Exhibit B - Transactions in the Stock by the Reporting Persons during the
last 60 days.
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 00753 P 103         SCHEDULE 13D               PAGE 7 OF 7 PAGES
- -----------------------                                  ---------------------

     After reasonable inquiry and to the best of my knowledge and belief, I
certify that the information set forth in this statement is true, complete and
correct.

Dated:  December 24, 1997

     BIOTECHNOLOGY VALUE FUND, L.P.

     By:  BVF Partners L.P., its general partner

          By:  BVF Inc., its general partner


               By:    /s/ MARK N. LAMPERT
                     ---------------------------------
                     Mark N. Lampert
                     President

     BVF PARTNERS L.P.

     By:  BVF Inc., its general partner


          By:    /s/ MARK N. LAMPERT
                -------------------------------------------
                Mark N. Lampert
                President

     BVF INC.


     By:    /s/ MARK N. LAMPERT
           -----------------------------------------------------
           Mark N. Lampert
           President

<PAGE>
 
                                   EXHIBIT A

                       AGREEMENT REGARDING JOINT FILING
                       --------------------------------


     The undersigned, Biotechnology Value Fund, L.P., a Delaware limited
partnership, and BVF Partners L.P., a Delaware limited partnership, and BVF
Inc., a Delaware corporation, hereby agree and acknowledge that the Amendment
containing the information required by Schedule 13D, to which this Agreement is
attached as an exhibit, is filed on behalf of each of them.  The undersigned
further agree that any further amendments or supplements thereto shall also be
filed on behalf of each of them.

Dated:  December 24, 1997

     BIOTECHNOLOGY VALUE FUND, L.P.

     By:  BVF Partners L.P., its general partner

          By:  BVF Inc., its general partner


               By:    /s/ MARK N. LAMPERT
                     ---------------------------------
                     Mark N. Lampert
                     President

     BVF PARTNERS L.P.

     By:  BVF Inc., its general partner


          By:    /s/ MARK N. LAMPERT
                -------------------------------------------
                Mark N. Lampert
                President

     BVF INC.


     By:    /s/ MARK N. LAMPERT
           -----------------------------------------------------
           Mark N. Lampert
           President

<PAGE>
 
                                   EXHIBIT B

              TRANSACTIONS IN THE STOCK BY THE REPORTING PERSONS
              --------------------------------------------------
                            DURING THE LAST 60 DAYS
                            -----------------------
<TABLE>
<CAPTION>
 
                                                     Price      
Settlement                  For the                   per      
  Date           By        Account of    Quantity    Share      Type of Trade   Broker
======================================================================================
<C>          <S>           <C>           <C>        <C>         <C>             <C>
  11/03/97   Partners      BVF              1,500     $9.2415   Purchase        DAKN
- --------------------------------------------------------------------------------------
  11/07/97   Partners      BVF              2,800     $9.0809   Purchase        DAKN
- --------------------------------------------------------------------------------------
  11/07/97   Partners      BVF Ltd.         4,000     $9.0809   Purchase        DAKN
- --------------------------------------------------------------------------------------
  11/10/97   Partners      BVF              2,600     $9.0865   Purchase        DAKN
- --------------------------------------------------------------------------------------
  11/28/97   Partners      BVF              2,100     $9.1786   Purchase        DAKN
- --------------------------------------------------------------------------------------
  12/01/97   Partners      BVF              4,500     $9.2500   Purchase        DAKN
- --------------------------------------------------------------------------------------
  12/08/97   Partners      BVF Ltd.         3,100     $9.2057   Purchase        DAKN
- --------------------------------------------------------------------------------------
  12/09/97   Partners      BVF             26,100     $9.3622   Purchase        DAKN
- --------------------------------------------------------------------------------------
  12/09/97   Partners      BVF Ltd.        15,000     $9.3622   Purchase        DAKN
- --------------------------------------------------------------------------------------
  12/10/97   Partners      BVF              2,400     $9.3750   Purchase        DAKN
- --------------------------------------------------------------------------------------
  12/11/97   Partners      BVF             11,400     $9.2500   Purchase        DAKN
- --------------------------------------------------------------------------------------
  12/11/97   Partners      PAL              5,000     $9.2500   Purchase        DAKN
- --------------------------------------------------------------------------------------
  12/11/97   Partners      BVF Ltd.        11,400     $9.2500   Purchase        DAKN
- --------------------------------------------------------------------------------------
  12/15/97   Partners      BVF              4,080     $9.0625   Purchase        PWJC
- --------------------------------------------------------------------------------------
  12/15/97   Partners      ILL10            3,000     $9.0625   Purchase        PWJC
- --------------------------------------------------------------------------------------
  12/15/97   Partners      PAL              3,000     $9.0625   Purchase        PWJC
- --------------------------------------------------------------------------------------
  12/15/97   Partners      ZPG              3,000     $9.0625   Purchase        PWJC
- --------------------------------------------------------------------------------------
  12/15/97   Partners      BVF Ltd.        11,455     $9.0625   Purchase        PWJC
- --------------------------------------------------------------------------------------
  12/16/97   Partners      BVF Ltd.         2,000     $9.0000   Purchase        DAKN
- --------------------------------------------------------------------------------------
  12/19/97   Partners      ILL10            3,000     $8.7500   Purchase        DAKN
- --------------------------------------------------------------------------------------
  12/19/97   Partners      PAL              3,000     $8.7500   Purchase        DAKN
- --------------------------------------------------------------------------------------
  12/19/97   Partners      BVF Ltd.         9,300     $8.7500   Purchase        DAKN
- --------------------------------------------------------------------------------------
 
DAKN         =             Dakin Securities
PWJC         =             Paine Webber
 
 
</TABLE>


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